disabled quality score conversion in FASTQ and Solexa

[biopieces.git] / bp_bin / read_solexa

diff --git a/bp_bin/read_solexa b/bp_bin/read_solexa
index c1b4f0ba1be06dbb945ceec512ee389ff7cef67b..0d93142097d3df871c735a55728d357a5b156411 100755 (executable)
--- a/bp_bin/read_solexa
+++ b/bp_bin/read_solexa
@@ -67,16 +67,6 @@ if ( $options->{ 'data_in' } )
     {
         if ( $record = Maasha::Fastq::fastq2biopiece( $entry ) )
         {
-            if ( not $options->{ 'skip_quality' } )
-            {
-                $record->{ 'SCORES' } =~ s/(\d+) ?/Maasha::Fastq::score2phred( $1 )/ge if $options->{ 'format' } eq 'decimal';
-                Maasha::Fastq::solexa2phred( $record->{ 'SCORES' } );
-                Maasha::Fastq::lowercase_low_scores( $record->{ 'SEQ' }, $record->{ 'SCORES' }, $options->{ 'quality' } );
-
-                $record->{ 'SCORES' }     =~ s/(.)/ord( $1 ) - 33 . ";"/ge; # http://maq.sourceforge.net/fastq.shtml
-                $record->{ 'SCORE_MEAN' } = sprintf( "%.2f", Maasha::Calc::mean( [ split /;/, $record->{ 'SCORES' } ] ) );
-            }
-
             Maasha::Biopieces::put_record( $record, $out );
         }